RNA-Seq experiment GSE30352

Experiment name

The evolution of gene expression levels in mammalian organs [GSE30352]

Source

GEO

Experiment description

Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes.

EST library 12093

Two different donor eyes (75-80 years old) yielded approximately 600 mg of dissected RPE/choroid tissue. This in turn yielded 340 ug of total RNA and 7 ug of mRNA. A directionally cloned cDNA library in the pCMVSPORT6 vector was constructed at Life Technologies (Rockville, MD; now part of Invitrogen Corp), essentially following the protocols of the SuperScript Plasmid System (Invitrogen Corp. <http://www.invitrogen.com/>). The library code designation was cs. For this library, cDNA inserts were cloned into the NotI/MluI sites of the vector. EST analysis was performed on the unamplified library at the NIH Intramural Sequencing Center (NISC).

EST library 628

1st strand cDNA was prepared from mRNA obtained from Clontech Laboratories, Inc., and primed with a Not I - oligo(dT) primer [5' TGTTACCAATCTGAAGTGGGAGCGGCCGCCCAATTTTTTTTTTTTTTTTT 3']. Double-stranded cDNA was ligated to Eco RI adaptors (Pharmacia), digested with Not I and cloned into the Not I and Eco RI sites of the modified pT7T3 vector. Library went through one round of normalization to Cot5, and was constructed by Bento Soares and M. Fatima Bonaldo.